• About Me

    I'm a PhD candidate in the Stajich Lab at University of California, Riverside. My work focuses on the evolution of sexual development in fungi. I would describe myself as an evolutionary developmental/cell biologist with a broad interest in the origin of cell type diversity and functional specialization, the evolution of gene regulatory networks in phyla with disparate body plans, and evolutionary innovations and origins of novel adaptive features. Traditionally, evolutionary biology drew on palaeontology, anatomy, and functional morphology, but has recently come to rely on genomics, cell biology, and developmental biology. These latter fields, while traditionally the realm of biomedical research, are of particular interest to me because they provide a new perspective that promises to reveal a new level of detail about the mechanism of evolution.


    Prior to starting my PhD studies, I was a laboratory programs assistant at the Denver Museum of Nature and Science. This position was part of the Museum Programs department which focuses on delivering positive educational experiences to guests through various types of programming. I was primarily involved with Biology Basecamp, a participatory lab within the Expedition Health Exhibit. In this space, guests were able to perform simple experiments where they were introduced to the tools of science and the scientific method. Through this position I participated in science communication and informal education. Alongside my PhD I have been developing my SciComm skills to improve public understanding and awareness of science as well as engagement with science.




    University of California Riverside

    PhD Candidate

    University of Denver

    MS Cell & Molecular Biology, 2013-2015

    University of Denver

    BS Molecular Biology, 2009-2013

    Minors: chemistry, mathematics
    Research: Taste bud ultrastructure, Kinnamon Laboratory


    Origin of Cell Type Diversity

    Multicellular organisms are made up of a diverse collection of cells which serve myriad functions. I'm interested in understanding the diversification of cell types in the opisthokont lineage (Fungi + Metazoa).

    Evolution of Functional Specialization

    Organisms can be deconstructed into a set of modules at various biological levels. I'm interested in taking an organismal approach to understanding how these modules were assembled in opisthokonts.

    Evolution of Genomes and Gene Regulatory Networks

    One such biological module are the genome and gene regulatory networks. GRNs determine cell identity and, by extension, tissue identity. GRNs act on the genome, and together they control the phenotype. I'm interested in how the two co-evolve to give rise to diverse body plans.

    Complexification / Simplification

    A common misconception is that evolution drives organisms to become more complex. While this is an observable trend, we also see cases of organisms being secondarily simplified upon diverging from a common ancestor which gave rise to a "complex" organism. I am interested in exploring genomic complexity/simplicity in the opisthokont lineage

    Hidden Biology

    Most of our understanding of "weird" organisms, is limited by what I like to call the Bilaterian Bias. Many of the established animal models tend to be familiar, like mice or flies. Hypotheses about evolution in other animal branches are limited by what we understand in the familiar systems; while it's a good starting point, we may be missing out on other interesting features.


    Differential gene expression in choanocytes of freshwater sponge

    Master's thesis research

    Developed a method to halt development of choanocytes. Performed RNSseq on groups of normal sponges and sponges without choanocytes to identify candidate choanoderm genes.

    Whole-mount in situ hybridization for freshwater sponges

    Master's thesis research

    To validate gene expression, I worked on developing a whole-mount in situ hybridization protocol drawing from various established protocols for Drosophila, Amphimedon, and planarians

    Evo-Devo of Fungi

    PhD research

    I'm currently working on understanding the evolution of sexual development in fungi. I am focusing my work on the Mucoromycetes but will eventually include other sexual molds.


    Crowdsourced analysis of fungal growth and branching on microfluidic platforms

    A. Hopke, A. Mela, F. Ellett, D. Carter-House, J. F. Peña, J. E. Stajich, et al.

    PLoS ONE 2021 16(9): e0257823 https://doi.org/10.1371/journal.pone.0257823

    Transcriptional Analysis of Coccidioides immitis Mycelia and Spherules by RNA Sequencing

    A. F. Carlin , S. Beyhan, J. F. Peña, J. E. Stajich, S. Viriyakosol, J. Fierer, and T. N. Kirkland

    J. Fungi 2021 7:366  https://doi.org/10.3390/jof7050366

    Conserved expression of vertebrate microvillar gene homologs in choanocytes of freshwater sponges

    J. F. Peña, A. Alié, D. J. Richter, L. Wang, N. Funayama, and S. A. Nichols

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